In those early months after the slaughter, as the stunned survivors confronted an existence saturated in pain and despair, a saying took hold in Rwanda: condemned to live.

It was heard from parents who saw their children butchered, from Tutsis who by some random stroke of fate eluded the Hutu machetes only to discover almost everyone they loved was dead. After the last genocide of the 20th century, they returned to their villages to be told they were the lucky ones. But many said they would have preferred to die than face a future haunted by what they knew.

"Surviving is not what we wanted to happen," said Madalena Mukariemeria, a few years after escaping a massacre of more than 11,000 Tutsis at a church in Kibuye, where her father was killed. "To have survived is not something to be happy about. We don't hear among the survivors that it was good to survive."

The almost unbearable suffering was made more acute for some Tutsis by seeing the murderers of their families walking freely on the streets or even living next door.

Rwanda still evokes passions far beyond its borders, not only over the genocide itself but about where the country is headed today under its authoritarian leader, President Paul Kagame, who is regarded by some as its saviour and others as an autocrat leading it on the path towards another tragedy. But, little noticed outside the country, hundreds of thousands of the genocide's survivors have gone on to reconstruct their lives in the two decades since that 100 days of frenzied killing.

In the early years, some mothers looked to their surviving children as the reason to go on. Others, who lost everyone, took in orphans in an attempt to rebuild a family. Mukariemeria did both. She cared for her own three children and seven orphans, among the few survivors of her and her husband's extended family. Still, the legacy of genocide continued to intrude.

"We had a girl we adopted who was raped during the genocide and got Aids and died. Another one met the killer of her father. She went and threw herself in the lake and drowned because of the pain of seeing him," she said.

Others sought peace in forgiveness. Louis Rutaganira survived the slaughter in the same church as Mukariemeria by hiding under the dead. His wife and three of his children did not. Shortly afterwards, Rutaganira was struggling to imagine the future living in a town where much of the Hutu population showed no great regret for the genocide.

Louis Rutaganira lost his wife and three children in the slaughter but has found peace in forgiveness. 'It is painful but necessary,' he said. Photograph: Andy Hall Andy Hall/pr

"Their only pity is self-pity," he said in 1997. "They don't show remorse. They are more ashamed than sorry, because most of their relatives are in prison and in Rwanda it's shameful not to kill Tutsis but to have one of your relatives in prison. People in this town want to cover up the responsibility."

A decade after the genocide, Rutaganira was more optimistic.

"For me, things changed completely," he said at the time. "I managed to get back our business and rebuild my house and get married again and have three children with my new wife."

But he continued to be haunted by the question of who among his fellow townspeople had wielded the weapons that killed his family. The answer came as the government sought to mould Rwandans into a different way of thinking.

A decade after the genocide, the country faced a daunting problem: its jails were stuffed with more than 150,000 Hutus accused of killings, overwhelming the justice system. It would take decades to try all accused so the government revived a traditional system known as gacaca, or grass courts, using rapidly trained local judges drawn from the decimated communities.

Gacaca melded justice with a form of truth and reconciliation that required the guilty to admit and apologise for their crimes, identify their accomplices and to say where the bodies were buried – a pressing issue for many survivors searching for the graves of murdered loved ones. In return, the survivors were expected to offer forgiveness and the courts to impose lesser sentences, often resulting in immediate release from prison.

The church where more than 11,000 Tutsis sought refuge. Photograph: Andy Hall Andy Hall/pr

Gacaca was a means of clearing out the jails and meeting the clamour for justice. But it was also intended to break the chain of hate and violence by preventing those with blood on their hands from denying their crimes to the next generation.

Rutaganira described the gacaca trial of the men who stripped his wife, Marie Claire, and cut off her limbs as "very hard". "It was shocking to hear the one who killed my wife saying he was the one who killed her. The ones who killed my children also confessed. They were very sincere," he said last year. "I accepted their apologies. It is painful but necessary. The killers are our neighbours now."

Mukariemeria, who runs a small shop close to the centre of town, has not forgiven the murderers. Gacaca permitted anyone to speak for or against an accused person and she used it to recount the horror at the church and the shock of watching her neighbours kill.

Mukariemeria has also served as a witness at the international tribunal trying the leaders of the genocide, including Clement Kayishema, the regional governor who ordered the church massacre. He is serving life. "This one person was responsible for thousands of killings. Prison for life is not enough. I wish they could kill him over and over for each life he took," she said.

Mukariemeria's anger is infused with fear that history could repeat itself. She has faith in Kagame as a strong leader who can keep Hutu extremists at bay but she is not persuaded the killers' apologies are sincere and she wonders what will happen after he leaves power. "We still live in fear but that's just the way it is," she said.

Kagame's plan for preventing another genocide has been to raise a new generation of Rwandans who think differently from their parents, and to rapidly reduce the poverty he regards as underpinning the ignorance, fear and hatred behind the massacres. Western governments poured aid into Rwanda to expand education, healthcare and access to electricity, and build new homes and roads. Foreign investment followed in hotels, mining, tea plantations and Chinese-built office blocks.

Washington and London praised Kagame as the Rwandan economy recorded 8% growth year after year. But even those close allies are now voicing disquiet that his firm leadership also includes the suppression of political opposition, a tight rein on the media and a string of killings and assaults on former allies who fled into exile.

None of that seems to worry Florence Bugemimana, a member of a youth group at the church where Rutaganira and Mukariemeria survived. She was born a year after the killings and is a product of the Rwandan government's efforts to raise a generation that understands the genocide as a massive crime that must never be repeated.

Bugemimana does not think the ideology of genocide is dead in Rwanda but she believes the crucial difference from 20 years ago is it is no longer promoted by those in positions of authority. "Some people still have that ideology but it's not easy for them to teach it as before. They can say it in their houses, but in the schools and on the radio and in the churches we hear something different," she said.

"It was a big lesson for all of us. The whole country. Everyone suffered. No one wants that again."

Chris McGreal's Chaplains of the Militia, on the role of the Catholic church during the genocide, is out now from Guardian Shorts. Visit guardianshorts.com to read an extract and find out more.

A majority parliamentary presence, constitutional support, a drive to tackle gender-based violence – post-genocide Rwanda seems a good place to be a woman. But the reality is more complex Alexandra Topping investigates